Traditional publishing is restrictive. The restriction comes from economic constraints on the publisher. Publishing has always been a few hits to lots of misses and the only way to eliminate the economic risk was an extreme conservative approach. Yes, many authors are feeling the liberation of not having to answer to those conservative publishing enclaves, but economics still govern.
The problem isn't being "branded" as a self published author, but rather the author never gets a brand. JA Konrath has a brand, "the self-publish" brand, which he has been cultivating for a couple of years quite successfully. This is why his books sell. Everyone knows who he is, even people who don't read his type of books.
Somewhere there is a happy in-between, a sweet spot where the author has freedom, the publisher allows it and readers get what they want and a lot of books get sold as everyone plays off each other's strengths and needs. I think that is the future and that the self-publishing pendulum will swing back until it is resting somewhere in the middle -- which is good news for the middleman.